Merge pull request #72 from KumarLabJax/repository-reorganization

Repository reorganization

Author: bergsalex

.github/workflows/_build-docker-action.yml

@@ -0,0 +1,50 @@
+name: 'Build Docker Image'
+on:
+  workflow_call:
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: aberger4/mouse-tracking
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Log in to Container Registry
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v3
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: aberger4
+        password: ${{ secrets.DOCKER_SECRET }}
+
+    - name: Extract metadata
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+        tags: |
+          type=ref,event=branch
+          type=ref,event=pr
+          type=semver,pattern={{version}}
+          type=semver,pattern={{major}}.{{minor}}
+          type=raw,value=latest,enable={{is_default_branch}}
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: ${{ github.event_name != 'pull_request' }}
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max

.github/workflows/_format-lint-action.yml

@@ -0,0 +1,33 @@
+name: 'Lint Code Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: 'Python version to set up'
+        required: false
+        default: '3.10'
+        type: string
+jobs:
+  format-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies with uv
+        run: uv sync --only-group lint
+
+      - name: Run Ruff Linter
+        run: uv run --only-group lint ruff check src/ tests/
+
+      - name: Run Ruff Formatter
+        run: uv run --only-group lint ruff format --check src/ tests/

.github/workflows/_run-tests-action.yml

@@ -0,0 +1,38 @@
+name: 'Python Tests Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: Python version to set up'
+        required: false
+        default: '3.10'
+        type: string
+      runner-os:
+        description: 'Runner OS'
+        required: false
+        default: 'ubuntu-latest'
+        type: string
+jobs:
+  run-tests:
+    runs-on: ${{ inputs.runner-os }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ inputs.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies with uv
+        run: uv sync --extra cpu
+
+      - name: Make Sure PyTorch is Installed
+        run: uv pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Test with pytest
+        run: uv run pytest tests

.github/workflows/pull-request.yml

@@ -0,0 +1,20 @@
+name: Pull Request Checks
+
+on:
+  pull_request:
+    branches: [ main, repository-reorganization ]
+
+jobs:
+  format-lint:
+    name: "Format and Lint"
+    uses: ./.github/workflows/_format-lint-action.yml
+
+  test:
+    name: "Run Tests"
+    needs: format-lint
+    uses: ./.github/workflows/_run-tests-action.yml
+
+  build:
+    name: "Build Docker Image"
+    needs: [format-lint, test]
+    uses: ./.github/workflows/_build-docker-action.yml

.gitignore

@@ -11,5 +11,4 @@
 __pycache__
 models
 work
-tests
 !mouse-tracking-runtime/models

Dockerfile

@@ -0,0 +1,21 @@
+FROM aberger4/mouse-tracking-base:python3.10-slim
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+ENV UV_SYSTEM_PYTHON=1 \
+    UV_PYTHON=/usr/local/bin/python \
+    PYTHONUNBUFFERED=1
+
+# Copy metadata first for layer caching
+COPY pyproject.toml uv.lock* README.md ./
+
+# Only install runtime dependencies
+RUN uv sync --frozen --no-group dev --no-group test --no-group lint --no-install-project
+
+# Now add source and install the project itself
+COPY src ./src
+
+RUN uv pip install --system .
+
+CMD ["mouse-tracking-runtime", "--help"]

README.md

@@ -7,19 +7,70 @@ This repository uses both Pytorch and Tensorflow Serving (TFS).
 
 # Installation
 
-Both Google Colab and singularity environments are supported. This environment is used because it is a convenient method to have both pytorch and tensorflow present.
+## Runtime Environments
 
-## Singularity Containers
+This repository supports both Docker and Singularity environments. 
 
-See the [container definition file](vm/deployment-runtime-RHEL9.def) in the vm folder. This container is based off a google colab public docker.
+The dockerfile is provided at the root of the repository ([Dockerfile](Dockerfile)), and the singularity 
+definition file is in the `vm` folder ([singularity.def](vm/singularity.def)).
+
+To learn more about how we support this, please read [vm/README.md](vm/README.md).
+
+## Development
+This repository uses [uv](https://uv.run/) to manage multiple python environments. 
+To install uv, see the [uv installation instructions](https://uv.run/docs/installation).
+
+To create the development environment, run:
+```
+uv sync --extra cpu
+```
+
+If you happen to have access to a GPU, you can create a GPU-enabled environment with:
+```
+uv sync --extra gpu
+```
 
 # Available Models
 
 See [model docs](docs/models.md) for information about available models.
 
+## Model Directory Configuration
+
+The model directory can be configured at runtime using environment variables or nextflow parameters:
+
+### Environment Variable
+Set the `MOUSE_TRACKING_MODEL_DIRECTORY` environment variable:
+```bash
+export MOUSE_TRACKING_MODEL_DIRECTORY=/path/to/your/models
+```
+
+### Nextflow Parameter
+Use the `--model_dir` parameter when running nextflow:
+```bash
+nextflow run main.nf --model_dir /path/to/your/models --input_batch video_batch.txt --workflow single-mouse
+```
+
+### Default Location
+By default, models are expected at `/kumar_lab_models/models/`. The directory structure should follow:
+```
+models/
+├── pytorch-models/
+│   ├── single-mouse-pose/
+│   ├── multi-mouse-pose/
+│   └── fecal-boli/
+└── tfs-models/
+    ├── single-mouse-segmentation/
+    ├── multi-mouse-segmentation/
+    ├── multi-mouse-identity/
+    ├── static-object-arena/
+    ├── static-object-food/
+    └── static-object-lixit/
+```
+
 # Running a pipeline
 
-Pipelines are run using nextflow. For a list of all available parameters, see [nextflow parameters](nextflow.config). Not all parameters will affect all pipeline workflows.
+Pipelines are run using nextflow. For a list of all available parameters, see 
+[nextflow parameters](nextflow.config). Not all parameters will affect all pipeline workflows.
 
 You will need a batch file that lists the input files to process.
 

docs/legacy/README.md

@@ -0,0 +1,5 @@
+The files in this directory are kept for reference from an earlier organization
+of the project.
+
+For the latest documentation, please refer to the main README.md file in the root 
+directory.